hdl:10013/epic.49967
publisher:10.1186/2041-1480-5-5

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains


Katayama, Toshiaki, Wilkinson, Mark D, Aoki-Kinoshita, Kiyoko F, Kawashima, Shuichi, Yamamoto, Yasunori, Yamaguchi, Atsuko, Okamoto, Shinobu, Kawano, Shin, Kim, Jin-Dong, Wang, Yue, Wu, Hongyan, Kano, Yoshinobu, Ono, Hiromasa, Bono, Hidemasa, Kocbek, Simon, Aerts, Jan, Akune, Yukie, Antezana, Erick, Arakawa, Kazuharu, Aranda, Bruno, Baran, Joachim, Bolleman, Jerven, Bonnal, Raoul JP, Buttigieg, Pier, Campbell, Matthew P, Chen, Yi-an, Chiba, Hirokazu, Cock, Peter JA, Cohen, K, Constantin, Alexandru, Duck, Geraint, Dumontier, Michel, Fujisawa, Takatomo, Fujiwara, Toyofumi, Goto, Naohisa, Hoehndorf, Robert, Igarashi, Yoshinobu, Itaya, Hidetoshi, Ito, Maori, Iwasaki, Wataru, Kalaš, Matúš, Katoda, Takeo, Kim, Taehong, Kokubu, Anna, Komiyama, Yusuke, Kotera, Masaaki, Laibe, Camille, Lapp, Hilmar, Lütteke, Thomas, Marshall, M, Mori, Takaaki, Mori, Hiroshi, Morita, Mizuki, Murakami, Katsuhiko, Nakao, Mitsuteru, Narimatsu, Hisashi, Nishide, Hiroyo, Nishimura, Yosuke, Nystrom-Persson, Johan, Ogishima, Soichi, Okamura, Yasunobu, Okuda, Shujiro, Oshita, Kazuki, Packer, Nicki H, Prins, Pjotr, Ranzinger, Rene, Rocca-Serra, Philippe, Sansone, Susanna, Sawaki, Hiromichi, Shin, Sung-Ho, Splendiani, Andrea, Strozzi, Francesco, Tadaka, Shu, Toukach, Philip, Uchiyama, Ikuo, Umezaki, Masahito, Vos, Rutger, Whetzel, Patricia L, Yamada, Issaku, Yamasaki, Chisato, Yamashita, Riu, York, William S, Zmasek, Christian M, Kawamoto, Shoko and Takagi, Toshihisa ;
Contact
pier.buttigieg [ at ] awi.de

Abstract

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.



Item Type
Article
Authors
Katayama, Toshiaki, Wilkinson, Mark D, Aoki-Kinoshita, Kiyoko F, Kawashima, Shuichi, Yamamoto, Yasunori, Yamaguchi, Atsuko, Okamoto, Shinobu, Kawano, Shin, Kim, Jin-Dong, Wang, Yue, Wu, Hongyan, Kano, Yoshinobu, Ono, Hiromasa, Bono, Hidemasa, Kocbek, Simon, Aerts, Jan, Akune, Yukie, Antezana, Erick, Arakawa, Kazuharu, Aranda, Bruno, Baran, Joachim, Bolleman, Jerven, Bonnal, Raoul JP, Buttigieg, Pier, Campbell, Matthew P, Chen, Yi-an, Chiba, Hirokazu, Cock, Peter JA, Cohen, K, Constantin, Alexandru, Duck, Geraint, Dumontier, Michel, Fujisawa, Takatomo, Fujiwara, Toyofumi, Goto, Naohisa, Hoehndorf, Robert, Igarashi, Yoshinobu, Itaya, Hidetoshi, Ito, Maori, Iwasaki, Wataru, Kalaš, Matúš, Katoda, Takeo, Kim, Taehong, Kokubu, Anna, Komiyama, Yusuke, Kotera, Masaaki, Laibe, Camille, Lapp, Hilmar, Lütteke, Thomas, Marshall, M, Mori, Takaaki, Mori, Hiroshi, Morita, Mizuki, Murakami, Katsuhiko, Nakao, Mitsuteru, Narimatsu, Hisashi, Nishide, Hiroyo, Nishimura, Yosuke, Nystrom-Persson, Johan, Ogishima, Soichi, Okamura, Yasunobu, Okuda, Shujiro, Oshita, Kazuki, Packer, Nicki H, Prins, Pjotr, Ranzinger, Rene, Rocca-Serra, Philippe, Sansone, Susanna, Sawaki, Hiromichi, Shin, Sung-Ho, Splendiani, Andrea, Strozzi, Francesco, Tadaka, Shu, Toukach, Philip, Uchiyama, Ikuo, Umezaki, Masahito, Vos, Rutger, Whetzel, Patricia L, Yamada, Issaku, Yamasaki, Chisato, Yamashita, Riu, York, William S, Zmasek, Christian M, Kawamoto, Shoko and Takagi, Toshihisa ;
Divisions
AWI Organizations > Infrastructure > Computing and Data Centre
AWI Organizations > Biosciences > Joint Research Group: Deep Sea Ecology and Technology
Primary Division
Organizations > AWI Organizations > Biosciences
Programs
Helmholtz Research Programs > PACES II (2014-2020) > TOPIC 4: Research in science-stakeholder interactions > WP 4.2: Channelling research data to enhanced data products
Helmholtz Research Programs > PACES II (2014-2020) > TOPIC 4: Research in science-stakeholder interactions > WP 4.3: Providing information – enabling knowledge
Primary Topic
Helmholtz Programs > Helmholtz Research Programs > PACES II (2014-2020) > TOPIC 4: Research in science-stakeholder interactions > WP 4.2: Channelling research data to enhanced data products
Peer revision
Peer-reviewed
Publication Status
Published
Eprint ID
43650
DOI 10.1186/2041-1480-5-5

Cite as
Katayama, T. , Wilkinson, M. D. , Aoki-Kinoshita, K. F. , Kawashima, S. , Yamamoto, Y. , Yamaguchi, A. , Okamoto, S. , Kawano, S. , Kim, J. D. , Wang, Y. , Wu, H. , Kano, Y. , Ono, H. , Bono, H. , Kocbek, S. , Aerts, J. , Akune, Y. , Antezana, E. , Arakawa, K. , Aranda, B. , Baran, J. , Bolleman, J. , Bonnal, R. J. , Buttigieg, P. , Campbell, M. P. , Chen, Y. a. , Chiba, H. , Cock, P. J. , Cohen, K. , Constantin, A. , Duck, G. , Dumontier, M. , Fujisawa, T. , Fujiwara, T. , Goto, N. , Hoehndorf, R. , Igarashi, Y. , Itaya, H. , Ito, M. , Iwasaki, W. , Kalaš, M. , Katoda, T. , Kim, T. , Kokubu, A. , Komiyama, Y. , Kotera, M. , Laibe, C. , Lapp, H. , Lütteke, T. , Marshall, M. , Mori, T. , Mori, H. , Morita, M. , Murakami, K. , Nakao, M. , Narimatsu, H. , Nishide, H. , Nishimura, Y. , Nystrom-Persson, J. , Ogishima, S. , Okamura, Y. , Okuda, S. , Oshita, K. , Packer, N. H. , Prins, P. , Ranzinger, R. , Rocca-Serra, P. , Sansone, S. , Sawaki, H. , Shin, S. H. , Splendiani, A. , Strozzi, F. , Tadaka, S. , Toukach, P. , Uchiyama, I. , Umezaki, M. , Vos, R. , Whetzel, P. L. , Yamada, I. , Yamasaki, C. , Yamashita, R. , York, W. S. , Zmasek, C. M. , Kawamoto, S. and Takagi, T. (2014): BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains , Journal of Biomedical Semantics, 5 (1), p. 5 . doi: 10.1186/2041-1480-5-5


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